New Beginnings
by insanereader3
Summary: "Last time I did this, I ended up a toddler." "She'll help you." "She belongs with us. With you. She's your daughter." "We've got things to do, you and me. We can go anywhere. Everywhere. You choose." "You're my daughter and we've only just started. You're gonna be great. You're gonna be more than great... You're gonna be amazing."
1. Prologue

**First story! Instead of doing a disclaimer every chapter, I'll just do the one at the beginning. I do not, and most likely never will, own Doctor Who. Constructive criticism welcome. Enjoy!**

The TARDIS could feel her Thief's pain. He was alone. So alone. And he wanted nothing more than to be alone. He hated to be alone, but now, he only wished that everything would leave him alone. That's what he told himself. That's what he told everyone, now.

She missed it when he would dash around her console and shout things, and grin madly just before he opened the doors. She missed the strays he would bring home, and their awe at her. _Bigger on the inside_, indeed.

She was floating around in deep space when she felt it. A few years away, but not far, there was something she had only seen in people that her Thief knew, or knows. The golden light, that warned of the changes. She opened the Time Vortex and hurtled through it. She found the source of the energy, and the beautiful light. She couldn't see it, but she sensed it. She materialized around the source, and felt the light subside and the person—was it person?—land in one of her bedrooms. She had been aiming for the console room, but no matter. This would make her Thief happy, she hoped. Bring back the life, the energy he had so long ago.

Everyone was gone. The pink and yellow human, who became something more. The other human… who had cared for her Thief, even when he didn't know. The fiery one, who became the DoctorDonna. The pretty one, and the orange one. The child of the TARDIS, who was never there for long, but she was almost always there. They were all gone now. They kept her Thief safe from himself. Now he had no one to keep him safe. But he would. A flesh and blood person, who wasn't forced to stay in one shape. The TARDIS would always find a way to protect her Thief. Her precious Doctor.


	2. Suspicions

When Jenny woke up she had no idea where she was. It was certainly a nicer floor to walk on barefoot, definitely better than pavement, seeing as she couldn't walk. The bed was much more comfortable, but comfy didn't matter, especially if she was in the hands of the enemy. She needed to find her father, or escape from enemy hands. Then everything would work out all right. For some reason, everything was so much bigger now, and she couldn't balance quite right. She wasn't even strong enough to hold a gun! Even though the Doctor had told her guns were bad, she still needed to protect herself. She assumed the lack of balance and the size problems were due to some drug her kidnapper had given her. She needed to get out, and find an antidote.

She looked out from the comfy bed, and saw the floor was a long ways away. 'No pain no gain,' she thought and rolled off. She suppressed a cry as she landed. She had landed on her hand, and her pinkie finger was bent back painfully. She gritted her teeth and pulled it into place. She walked over to the door, attempting to be stealthy and pulled herself up. She grasped the handle and pulled. To her surprise it opened. She had thought her kidnapper would have at least locked her door. She set off down the corridor, and in no time she was completely lost. 'Keep turning left.' Jenny thought to herself. That's what you did with mazes. About an hour later, she ended up in the same the room she had been in yesterday. Not the one with the bed, but the one with the cold floor. Across the room, the man walked down a flight of stairs.

"Hello Jenny!" he waved cheerfully.

How did her kidnapper know her name? More importantly, he didn't appear to be armed. She could probably take him, as long as he didn't have back-up.

"What did you drug me with?" she demanded, and even to her ears, her voice was high-pitched and sounded like a child.  
To her surprise, the man answered, even though the answer didn't make sense. "I didn't drug you with anything."

"Then why is everything so big? My balance is off too. Did you do that?"

"Everything is so big, because you are a few feet smaller, and your balance is off because your physical body isn't used to being that size. Just give it a few days. I'm the Doctor."

"No you aren't," she argued; "you don't look like him!"

"And you don't look like the Jenny I knew." He countered. "We both regenerated." Under his breath he muttered something about her not knowing what that was. "When we get hurt, we change, and look different, and even think differently sometimes, you got shot, I absorbed some radiation after falling through a sky light." He shrugged. "Here's a mirror."

The space in front of Jenny became reflective, and she could see herself. Only, she didn't look right. She was tiny, the size of a child. She was wearing the same shirt she had worn last. Her hair was blonde, still, and a complete mess. She looked like a two or three-year old, in human time.

Jenny believed the man. He just seemed… good. Trustworthy. She was even becoming comfortable with the idea of looking different, but if she couldn't run, she'd go mad. The doctor watched her carefully for a reaction. She turned away from the mirror, and sat down. He sat down facing to her. "I'm going to show you what happened to me. And why I look different." he put his fingers to her temples, and before she could jerk away, his eyes closed, and the room around her spun, and she was somewhere else. Her father was there. She wanted to run and hug him, but she couldn't move.

His face was cut up, and when he ran his hands down his face, the cuts disappeared. "It's starting." he said to another, older man.

The scene changed, and her father was standing in a futuristic-y room, that looked sort of similar to the room she was in. He looked at his hands, and they were surrounded by a swirling golden light.

"I don't want to go." he said, and his voice sounded broken. He threw his arms back and as the light changed him into the man who said he was the Doctor the room around him collapsed and bits of the wall fell down. The lights disappeared and a different man was standing there.

"Legs! Still got legs! Good. Arms! Hands, ooh fingers, lots of fingers, ears yes, eyes, nose… I've had worse. Chin, blimey. hair, I'm a girl! No…no, I'm not a girl… and still not ginger! Something else, something important, I'm… I'm… I'm, ha-ha crashing! Ha-ha! Hoo-hoo! Ah! Geronimo!"

She was pulled back to the present and as she tried to stand up, she toppled over. The man was watching her cautiously. She sat up and leaned against the handrail.

"Where's Donna?" she asked.

He smiled sadly. "She's gone. She took my head into hers, and no human is meant to do that. I had to wipe her mind. Every mention of me, the TARDIS, even you, had to go. Otherwise she would burn up and die."

"Martha?"

"She found someone else. She lives on earth."

"So you're alone now?" Jenny asked.

"Yeah. Just me and the TARDIS."

"I've been trying to find you" Jenny admitted. "I travelled for a few years, but I got lonely. I'm 6 now."

"You look like a three-year old. Not many people ever manage to find me. Especially now."

"Why now in particular?"

"I…lost some of my dear friends. I don't get out much, now. Just me and the TARDIS."

She bit her lip.  
"You can stay with me, if you want. For as long as you want. After all, what kind of parent would I be if I left you out on the street?" he smiled.  
"A pretty lousy one." Jenny felt like dancing.

"That's settled then." he smiled.

Jenny yawned. She was tired, and more than a bit hungry. But sleep was definitely first priority. The Doctor scooped her up and carried her back to room she had woken up inside. He set her on the bed.

"Tomorrow, we'll get it furnished however you like." he promised.

He flicked the light-switch and the room went dark, except for a little nightlight in the corner Jenny hadn't noticed before. The Doctor shut the door with a soft 'snick', and Jenny heard his footsteps walked away. She snuggled under the covers, and sighed contentedly. Everything was working out after all.


	3. Settling In

When Jenny woke up, she felt at peace, for the first time in her fairly short life. She knew she had a way of getting food, she wasn't dodging bullets, and she knew where her father was. Saying that sent a jolt of excitement through her. How many people she knew, actually knew their father? She didn't know many people, but Jenny was positive that the number was few.

When she got tired of lounging in her (she had something she could actually call hers!) comfy bed, there was a matter of getting down. When she was bigger, she could have jumped, but Jenny didn't want a repeat of yesterday's fiasco, and so she formulated a plan. She pushed her pillow off the bed, and carefully calculated her landing to insure that she would definitely land on the pillow. She counted to three and rolled off. She landed on her cushy pillow, and was proud her plan had worked properly.

She slid off the pillow onto the floor, and walked to the door. She grabbed the handle, and pulled down, and pushed out. The door swing open and she tottered out. She needed to learn how to walk properly. With a growing feeling of horror, she realized that is she couldn't walk normally, she couldn't run. And if she couldn't run, then she had some big problems.

She moved down the metal hall, and like yesterday, she got lost. She knew that trying to shout would result in the Doctor running to her, but she knew that she would need to learn to navigate the complex hallways systems. Not today, though. She shouted "Hey!" and around her, the room disappeared and deposited her into the main control room. Jenny smiled. Her plan was a success. And even better, her father was there.

He grinned at her. "We need to get you cleaned up. You're a mess! How long has it been since you've had a bath? Don't answer that. You need new clothes too. And, we need to get your bedroom fixed up." he looked at her, and she nodded.

"Hope you like lots of bubbles!" he smiled, and Jenny thought about telling him that she had the thought process of a much older person, but decided that bubbles—whatever they were—were more important than acting older than she looked (or actually was, for that matter).

He led her to a large bathroom, and turned on the faucet. "If you need anything, shout." He smiled, and left the bathroom. She climbed into the tub and put some soap into her hair. As an afterthought, she pulled her too-big shirt off, and swished it around in the soapy water. Fascinated by the amount of dirt that came off; she wrung it out, and placed it on the floor near the tub. She drained the water, and climbed out. She grabbed a towel, and wrapped herself in it. Opening the door, she stuck her head out, and started down the hallway towards what she hoped was her bedroom.

After through a minute, the door she was walking past slid open, and the Doctor walked out.

"Hello." He said pleasantly, and she smiled at him. "Your bedroom's actually this way." He pointed down a corridor. He strode off, leaving Jenny almost running to catch up. He opened the door with a flourish, and she stepped into the room. The Doctor walked over to a wooden closet.

"The TARDIS knows what size you are, and if I might add, she's also wonderfully fashionable." he whispered the last part to Jenny and winked. The TARDIS hummed and he grinned. In the closet, there were lots of clothes. All the clothes were small, but so was she, now. Jenny picked out a blue shirt, and black leggings with a grey skirt. Her father had raised an eyebrow, but refrained from commenting.

Jenny explained the dilemma of the bed's height to her father.

"Of course we can fix that. Any color in particular?" he asked.

"Green! And blue." She added. "Will it still be comfy?"

The Doctor looked affronted. "Of course it will be comfy! What's the point of an uncomfortable bed?"  
Jenny agreed whole-heartedly.  
He grinned. "Coming up!"

Later that day, the Doctor and Jenny were sitting on stools in the kitchen. He was eating a banana, and she was attempting to pick up cheerios with her new fingers. She held them up in front of her face.

"Dad, how long will it be until I can be normal sized?"

He put down his banana. "You are normal sized, your regeneration just turned out looking…young. You still think like an adult, but you might have a few times where you act like a kid. For me, this regeneration turned out fairly young."

"But how long? I need to be able to run." She told him impatiently.

He thought for a moment. "It will probably be a few years until you've grown to full size, but you should be able to run and jump, judging by the fact that you look like a three year old."

The Doctor continued on "Time Lords have a longer lifespan than humans, so you shouldn't worry too much about losing time or anything."  
Jenny grimaced. She had been in top physical condition a few days ago, and now she was two feet tall. But it was already beginning to feel normal. Like, she couldn't imagine being any taller than she was now. She yawned. She suspected she had only gotten a few hours of sleep last night. If it could be called night.

The Doctor noticed, and stood up. "Time for bed!" He announced.

Jenny allowed herself to be carried down a dozen corridors to her room. The door was wooden, and a little chalk sign on the door said 'Jenny's Room'. The Doctor pulled the door open, and walked in. The ceiling was white, and so was the trim. The queen bed was low, so she could roll out, and not get hurt. The dresser was white, and there was a short bedside table with a lamp. He set Jenny down on her bed, and she blinked up at him sleepily.

"Goodnight" She murmured.

"Goodnight." He kissed her forehead, and stood up. He walked to the door and turned the light off. In the light from the hallway, he could see her, and he lingered moment, before closing the door, and walking away.


	4. Omelettes

**Okay! Sorry for the wait, just fixing some plot-related problems. We have another filler or two, then the plot shall commence! Enjoy.**

While Jenny was sleeping, the Doctor was sitting in the swing under the console. He'd taken off his tweed jacket so he could patch up a few bits and bobs of the TARDIS. He petted the spaceship lovingly.

"Thanks for bringing her here, Old Girl. Means a lot to me." he said aloud.

The TARDIS hummed, and a beeping noise informed him that there was a new room. He grinned. The TARDIS was sentient, and knew exactly what her occupants needed. She had made a playroom, for Jenny. And although she would no doubt protest at having one, the Doctor figured she could do with a little bit of childhood, to make up for her lost years.

The TARDIS had also moved Jenny's room closer to the main control room, so she couldn't get lost on her way. As Time Lords grew older, they needed less and less sleep, so he might make do with a few hours a week, but Jenny would need about 8 hours a day. 'Just like a human' he thought with a smile. But there wouldn't be any humans on the TARDIS for a long time. He didn't need any more loss.

He pulled two wired together and they sparked. He held them with one hand and used his sonic to weld them together with the other. He was fixing the 'cloaking device'. That would keep prying eyes off the TARDIS for a good while. He could have fixed the Chameleon Circuit, but he loved his ship's blue box too much to let it go. Jenny would need time to adjust to being small. He knew River had ended up a toddler, during one of her regenerations, and she had said it had taken some time to adjust.

Several minutes later, a door slid open, and Jenny walked through. She walked around the console, and the Doctor grinned up at her through the glass. Her feet were bare, and she smiled down at him. The Doctor stood, and mounted the stairs. She barely came to above his knee at her full standing height. He lifted her up from under her arms and swung her around. Jenny giggled, and the Doctor grinned. They paraded down the hall to the kitchen. He set her in a high chair, and sat himself down in a spinney chair.

"What's for breakfast?" he asked her.

Jenny glanced around the TARDIS's fully stocked kitchen. Her eyes rested on the Twenty-First-Century-Earth-style refrigerator. The Doctor followed her eyes, and then decided for her. "Omelettes!"

He stood and ran around the kitchen, opening and closing the fridge door, shouting in French, and throwing eggshells everywhere. About 5 minutes later, he was seated, and stabbing a gooey mess of eggs and cheese with a fork.

Jenny watched him for a moment, and then imitated the way he was holding the fork. She speared a chunk of eggs, and put it in her mouth. She made a face.

He noticed. "Is it alright? Do you need any salt?"

"It tastes… different. Different than I thought it would."

He glanced up. "Different good? Or different bad?" he asked around the food he was chewing.

Jenny took another bite. "I can't decide… What kind of food is it?"

"Earth food. You know, I was there. Mid-sixteenth century, they were calling it something… French, I suppose, and I took a look at it, and said, 'That's an omelettle!" I'd assume they stared using that, 'cause I haven't heard it called otherwise since. You should have seen the size of the omelette Napoleon had made for him and his army. He got every egg in the whole village, and made a huge omelette! South-western France, Bessières, I think."

She stared at him for a moment. "Who's Napoleon?"

He waved his hand. "French military and political leader. He had a ridiculously short temper. He was 1.7 meters tall, and had a fabulous hat… you know, I'd love a hat like that. I should really get one some time."

Jenny looked interested. "Maybe we can go see it some time. Earth sounds like fun." She hesitated. "Where is it?"

"You probably know it as Sol. 3. Milky Way galaxy."

She brightened. "I think I've been there."

The Doctor looked intrigued. He pushed his plate away, omelette forgotten. "Really? Why?"

"I don't know, looking for you, I think. It's funny, because I don't actually remember it too well." She frowned. "I feel like it was the last place I went before coming here, but I might be wrong."

They were both silent for a moment, until Jenny brightened. "Come on, let's go exploring. I bumped into the park on the way here." She pushed back her chair, and hopped down. She ran down the hallway, and beckoned for him to follow her.

"If you see the swimming pool, tell me! I haven't seen it for ages!" He called after her.

Jenny saluted, and kept running, until she was out of sight. The Doctor watched, and tried to remember his childhood. It was hardly a childhood. 'More like an alien boot camp' he thought bitterly. He shook his head and smiled. Jenny's childhood—if it was that—was going to be very different, if he had anything to say about it.


	5. Introductions

**Alright! Sorry for the wait. Was going to post this yesterday, but I had some difficulty logging on. Anyways, enjoy!**

It had been what felt like forever since Jenny had been drawn to the TARDIS. And she loved every minute of it. Jenny had almost mastered the art of not getting lost in the TARDIS. She could make her way to her room, the kitchen, then the pool, and back to the console, all in under 10 minutes. Any child could see how happy the Doctor was. He doted on her, and always gave her his full attention. Jenny felt special whenever he praised her, or smiled at her. She felt sure any sane person in the universe would be jealous.

Today, her father had promised to teach her how to fly the TARDIS. She figured that if she needed to make a getaway or something, it be a useful skill to have. The Doctor was dressed in his blue shirt with red suspenders, and a bow-tie. She wasn't sure why he liked bow-ties so much, but she figured he was allowed to have a few strange quirks.

"Alright!" He shouted as he entered the console room. He flipped a few switched and pushed a blue button. "Just taking it down to basic for you." He told her as a powering down hum emanated from the TARDIS.

Jenny wasn't entirely sure what that meant, but she watched carefully, in case she would ever need to do that. The Doctor stepped back, looking pleased.

"Okay, so pull that lever…" he instructed. She did, and the ship rocked from side to side, and the Doctor's tea sloshed around in his mug. "…and stand right here, and pull the zigzag plotter."

"Why do I have to stand right there?" she asked, even as she moved over to the spot he was pointing at.

"Because otherwise it doesn't work, and we'll go hurtling into the Time Vortex, and I'd have no idea where we would end up." He grinned at her, even though that sounded terrible.

Suddenly, they were both thrown back. Jenny landed on the jump seat, and the Doctor caught himself on the railing. He dashed over to the monitor screen, and groaned.

"What is it? What happened?"

"Where going to the last place she landed. I told you to press the wrong button. I meant for you to press the stabilizers…" He was muttering under his breath and looked flustered.

"Where are we going?"

"Stormcage."

"Where's that?"

"Jenny, you need to understand something." He continued on to tell her that he was married. Also, the fact that the woman he was married to was the daughter of his 'lost' (he didn't specify how) human best friends, and was a little bit (okay, a lot) Time-Lord, due to the TARDIS, and a religious movement, but most importantly was in jail for his murder, bothered her.

"You're married, to a psychopath, who was stolen from her parents as a young child, and raised for the sole purpose of killing you?" Jenny clarified.

"Yes. If it helps, she didn't actually kill me. She shot a robot replica of me, and then we got married in an aborted timeline."

"Not helping!" she muttered.

The Doctor winced. "Sorry."

Jenny was upset. Donna, _the woman who had named her_, didn't even remember her or her father, and her father was married to a woman who was apparently a psychopath.

"Are you sure?" She wasn't even sure what she was asking about. He had to be kidding.

"Yes. She would have let the universe disintegrate just because she refused to kill me."

Jenny massaged her temples. This was making her head hurt.

"Why are you telling me this?"

"Because we're headed to the containment facility she is at in this point in her timeline."

"So…We're _actually_ going outside the TARDIS?"

"Yeah, but don't go telling people you have two hearts."

"I won't."

"Now let's get you some shoes. Can't have you going around outside barefoot The Old Girl isn't letting me out of this, so I suppose I'm going to have to put on a brave face.!" the Doctor donned his tweed jacket. He walked over to a little cabinet that was in the wall. He swing open the hexagon shaped door and peered in.

"Which shoes do you want?" He shouted.

"The red ones!" She called.

The Doctor grabbed the shoes and slid her feet into the red trainers and laced them up. They were almost the same as her father's tenth regenerations shoes. Good for running.

Jenny jumped up into a chair and gripped the handrails as the Doctor danced around the console, flicking switches and pulling levers. There was a jolt, and a strange noise as the TARDIS materialized.

"Stay here. I need to check and make sure River knows I know who she is yet."

None of this made sense to Jenny, and she started to protest as he sprinted to the doors and flung them open. She could barely see out, and she craned her neck to see a little more of outside. She heard the Doctor talking quickly, and she caught the words; time, explain, daughter, tenth regeneration, and then there was a click. Jenny recognized the sound of a gun being cocked.

Jenny glanced down. She was confident she could jump and land fine. She took a breath, and jumped, landing almost perfectly. She tottered over to the door, and kept her back to the door, so people wouldn't be able to see her. She edged toward the door, and heard a woman's voice say, "Come out sweetie!" and she moved a little faster. She stepped into the light to assess the situation. Her father had his arms slightly raised, in a placating gesture and behind bars; there was a woman with curly blond hair pointing a gun at his head.

"Hello sweetie." she smiled at Jenny. To the Doctor she said in a voice cold as ice "Twenty seconds. Talk fast."

The Doctor looked annoyed. "River, put the gun down. Can I explain in the TARDIS?"

River crossed her arms. "No."

He glanced at Jenny. She was itching to do something. She used her eyes to plead, and he shook his head at her. He turned to River.

"In my tenth regeneration, I visited the planet Messaline. There were humans there, and they were in the middle of a war. They needed more soldiers, so they were using a machine, a progenitor, for reproduction from a single organism. It means one parent is biological mother and father. They took a sample of diploid cells, split them into haploids, then recombined them in a different arrangement and grew. Very fast, to create a full-grown human, complete with training in combat and warfare." he paused and looked at River to make sure she was following. She nodded.

"They took a sample of my flesh, and Jenny came out. She was later killed, or so I thought. I left the planet. Unbeknownst to me, Jenny was revived. She's a Time Lord, since she has just my DNA. She didn't regenerate though. She left the planet in search of me, and a few years later, she was shot, and regenerated into her current body."

"That was 44 seconds."

"Less than a minute." he shrugged.

"More than twenty seconds." She peered at Jenny. "She kind of looks like you."

"Really?"

"No. But she might have. Regeneration and all." She addressed Jenny. "Once I regenerated into a toddler with dark skin. I grew up with my parents. They named me after me."

Jenny didn't reply.

River looked dubious. "Any proof? 'Cause for all I know, she could be wearing a perception filter. She could be anything!"

The Doctor fished a stethoscope out of his pocket. He tossed it to River. "Listen." he pulled Jenny a little closer to the bars. River put it in her ears, and held the metal disk to the left of Jenny's chest, then the right.

"Two hearts." she murmured. The Doctor grinned. He counted to three in his head.

"Let me out. Right now."

The Doctor pulled Jenny back and pointed his conic screwdriver at the door. It slid open, and River walked out and threw her arms around him in a hug. Jenny stood uncertainly to the side. River smiled down at her.

"Come here, you," she said and kneeled to hug Jenny tightly. The Doctor grinned at her and Jenny grinned back at him over Rivers shoulder. River released her and stood.

"Have you told my lovely parents yet?" she raised an eyebrow.

The Doctor stopped smiling. He looked deadly serious. "River, have we done Manhattan yet?"

River grinned and flipped her hair. "Ooh! America!"

He looked at a loss for words. Finally, he sighed. "Why don't we go on a picnic? Just for some family bonding time. Jenny's been wanting to see Earth, and I know a great place for tea." He smiled, but even to Jenny it looked fake. If River noticed, she didn't say anything.

"Come on, then!" she called over her shoulder, as she pulled the doors open. "We're off."

**Okay! River won't be here for long (unfortunately) but I do have some family bonding planned for the next chapter.**


End file.
